Analysis and Automated Discovery of Attacks in Transport Protocols

Transport protocols like TCP and QUIC are a crucial component of today’s Internet, underlying services as diverse as email, file transfer, web browsing, video conferencing, and instant messaging as well as infrastructure protocols like BGP and secure network protocols like TLS. Transport protocols provide a variety of important guarantees like reliability, in-order delivery, and congestion control to applications. As a result, the design and implementation of transport protocols is complex, with many components, special cases, interacting features, and efficiency considerations, leading to a high probability of bugs. Unfortunately, today the testing of transport protocols is mainly a manual, ad-hoc process. This lack of systematic testing has resulted in a steady stream of attacks compromising the availability, performance, or security of transport protocols, as seen in the literature. Given the importance of these protocols, we believe that there is a need for the development of automated systems to identify complex attacks in implementations of these protocols and for a better understanding of the types of attacks that will be faced by next generation transport protocols. In this dissertation, we focus on improving this situation, and the security of transport protocols, in three ways. First, we develop a system to automatically search for attacks that target the availability or performance of protocol connections on real transport protocol implementations. Second, we implement a model-based system to search for attacks against implementations of TCP congestion control. Finally, we examine QUIC, Google’s next generation encrypted transport protocol, and identify attacks on availability and performance

Motif discovery in sequential data

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2006.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (v. 2, leaves [435]-467).In this thesis, I discuss the application and development of methods for the automated discovery of motifs in sequential data. These data include DNA sequences, protein sequences, and real-valued sequential data such as protein structures and timeseries of arbitrary dimension. As more genomes are sequenced and annotated, the need for automated, computational methods for analyzing biological data is increasing rapidly. In broad terms, the goal of this thesis is to treat sequential data sets as unknown languages and to develop tools for interpreting an understanding these languages. The first chapter of this thesis is an introduction to the fundamentals of motif discovery, which establishes a common mode of thought and vocabulary for the subsequent chapters. One of the central themes of this work is the use of grammatical models, which are more commonly associated with the field of computational linguistics. In the second chapter, I use grammatical models to design novel antimicrobial peptides (AmPs). AmPs are small proteins used by the innate immune system to combat bacterial infection in multicellular eukaryotes. There is mounting evidence that these peptides are less susceptible to bacterial resistance than traditional antibiotics and may form the basis for a novel class of therapeutics.(cont.) In this thesis, I described the rational design of novel AmPs that show limited homology to naturally-occurring proteins but have strong bacteriostatic activity against several species of bacteria, including Staphylococcus aureus and Bacillus anthracis. These peptides were designed using a linguistic model of natural AmPs by treating the amino acid sequences of natural AmPs as a formal language and building a set of regular grammars to describe this language. is set of grammars was used to create novel, unnatural AmP sequences that conform to the formal syntax of natural antimicrobial peptides but populate a previously unexplored region of protein sequence space. The third chapter describes a novel, GEneric MOtif DIscovery Algorithm (Gemoda) for sequential data. Gemoda can be applied to any dataset with a sequential character, including both categorical and real-valued data. As I show, Gemoda deterministically discovers motifs that are maximal in composition and length. As well, the algorithm allows any choice of similarity metric for finding motifs. These motifs are representation-agnostic: they can be represented using regular expressions, position weight matrices, or any other model for sequential data.(cont.) I demonstrate a number of applications of the algorithm, including the discovery of motifs in amino acids and DNA sequences, and the discovery of conserved protein sub-structures. The final chapter is devoted to a series of smaller projects, employing tool methods indirectly related to motif discovery in sequential data. I describe the construction of a software tool, Biogrep that is designed to match large pattern sets against large biosequence databases in a parallel fashion. is makes biogrep well-suited to annotating sets of sequences using biologically significant patterns. In addition, I show that the BLOSUM series of amino acid substitution matrices, which are commonly used in motif discovery and sequence alignment problems, have changed drastically over time.The fidelity of amino acid sequence alignment and motif discovery tools depends strongly on the target frequencies implied by these underlying matrices. us, these results suggest that further optimization of these matrices is possible. The final chapter also contains two projects wherein I apply statistical motif discovery tools instead of grammatical tools.(cont.) In the first of these two, I develop three different physiochemical representations for a set of roughly 700 HIV-I protease substrates and use these representations for sequence classification and annotation. In the second of these two projects, I develop a simple statistical method for parsing out the phenotypic contribution of a single mutation from libraries of functional diversity that contain a multitude of mutations and varied phenotypes. I show that this new method successfully elucidates the effects of single nucleotide polymorphisms on the strength of a promoter placed upstream of a reporter gene. The central theme, present throughout this work, is the development and application of novel approaches to finding motifs in sequential data. The work on the design of AmPs is very applied and relies heavily on existing literature. In contrast, the work on Gemoda is the greatest contribution of this thesis and contains many new ideas.by Kyle L. Jensen.Ph.D

Computer Aided Verification

This open access two-volume set LNCS 10980 and 10981 constitutes the refereed proceedings of the 30th International Conference on Computer Aided Verification, CAV 2018, held in Oxford, UK, in July 2018. The 52 full and 13 tool papers presented together with 3 invited papers and 2 tutorials were carefully reviewed and selected from 215 submissions. The papers cover a wide range of topics and techniques, from algorithmic and logical foundations of verification to practical applications in distributed, networked, cyber-physical, and autonomous systems. They are organized in topical sections on model checking, program analysis using polyhedra, synthesis, learning, runtime verification, hybrid and timed systems, tools, probabilistic systems, static analysis, theory and security, SAT, SMT and decisions procedures, concurrency, and CPS, hardware, industrial applications

Syntax-based machine translation using dependency grammars and discriminative machine learning

Machine translation underwent huge improvements since the groundbreaking introduction of statistical methods in the early 2000s, going from very domain-specific systems that still performed relatively poorly despite the painstakingly crafting of thousands of ad-hoc rules, to general-purpose systems automatically trained on large collections of bilingual texts which manage to deliver understandable translations that convey the general meaning of the original input. These approaches however still perform quite below the level of human translators, typically failing to convey detailed meaning and register, and producing translations that, while readable, are often ungrammatical and unidiomatic. This quality gap, which is considerably large compared to most other natural language processing tasks, has been the focus of the research in recent years, with the development of increasingly sophisticated models that attempt to exploit the syntactical structure of human languages, leveraging the technology of statistical parsers, as well as advanced machine learning methods such as marging-based structured prediction algorithms and neural networks. The translation software itself became more complex in order to accommodate for the sophistication of these advanced models: the main translation engine (the decoder) is now often combined with a pre-processor which reorders the words of the source sentences to a target language word order, or with a post-processor that ranks and selects a translation according according to fine model from a list of candidate translations generated by a coarse model. In this thesis we investigate the statistical machine translation problem from various angles, focusing on translation from non-analytic languages whose syntax is best described by fluid non-projective dependency grammars rather than the relatively strict phrase-structure grammars or projectivedependency grammars which are most commonly used in the literature. We propose a framework for modeling word reordering phenomena between language pairs as transitions on non-projective source dependency parse graphs. We quantitatively characterize reordering phenomena for the German-to-English language pair as captured by this framework, specifically investigating the incidence and effects of the non-projectivity of source syntax and the non-locality of word movement w.r.t. the graph structure. We evaluated several variants of hand-coded pre-ordering rules in order to assess the impact of these phenomena on translation quality. We propose a class of dependency-based source pre-ordering approaches that reorder sentences based on a flexible models trained by SVMs and and several recurrent neural network architectures. We also propose a class of translation reranking models, both syntax-free and source dependency-based, which make use of a type of neural networks known as graph echo state networks which is highly flexible and requires extremely little training resources, overcoming one of the main limitations of neural network models for natural language processing tasks